FMO DATABASE

FMODB ID: G6V31

Calculation Name: 5WMF-A-Xray372

Preferred Name: Epstein-Barr nuclear antigen 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5WMF

Chain ID: A

ChEMBL ID: CHEMBL1293281

UniProt ID: P03211

Base Structure: X-ray

Registration Date: 2023-06-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	137
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1148098.656669
FMO2-HF: Nuclear repulsion	1094804.643609
FMO2-HF: Total energy	-53294.01306
FMO2-MP2: Total energy	-53447.429244

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:475:ASN)

Summations of interaction energy for fragment #1(A:475:ASN)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-18.405	-18.769	17.893	-8.983	-8.546	-0.088

Interaction energy analysis for fragmet #1(A:475:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.019

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	477	LYS	1	0.964	0.969	3.726	1.104	2.361	0.006	-0.624	-0.639	0.002
4	A	478	PHE	0	-0.025	-0.005	2.722	-0.262	1.100	0.167	-0.547	-0.982	0.004
5	A	479	GLU	-1	-0.691	-0.859	1.963	-24.692	-27.982	17.723	-7.788	-6.645	-0.094
6	A	480	ASN	0	-0.022	-0.016	4.963	1.277	1.413	-0.001	-0.009	-0.127	0.000
7	A	481	ILE	0	-0.045	-0.007	7.422	0.592	0.592	0.000	0.000	0.000	0.000
8	A	482	ALA	0	0.031	0.018	7.202	0.370	0.370	0.000	0.000	0.000	0.000
9	A	483	GLU	-1	-0.795	-0.859	8.097	-0.805	-0.805	0.000	0.000	0.000	0.000
10	A	484	GLY	0	-0.004	0.008	10.688	0.233	0.233	0.000	0.000	0.000	0.000
11	A	485	LEU	0	-0.012	-0.012	11.676	0.126	0.126	0.000	0.000	0.000	0.000
12	A	486	ARG	1	0.822	0.871	10.822	1.080	1.080	0.000	0.000	0.000	0.000
13	A	487	ALA	0	0.007	0.010	14.518	0.101	0.101	0.000	0.000	0.000	0.000
14	A	488	LEU	0	-0.024	-0.012	16.735	0.068	0.068	0.000	0.000	0.000	0.000
15	A	489	LEU	0	-0.019	-0.009	15.663	0.039	0.039	0.000	0.000	0.000	0.000
16	A	490	ALA	0	-0.012	-0.002	18.686	0.041	0.041	0.000	0.000	0.000	0.000
17	A	491	ARG	1	0.771	0.870	20.468	0.372	0.372	0.000	0.000	0.000	0.000
18	A	492	SER	0	-0.034	-0.023	23.017	0.028	0.028	0.000	0.000	0.000	0.000
19	A	493	HIS	0	0.000	0.017	23.689	-0.029	-0.029	0.000	0.000	0.000	0.000
20	A	494	VAL	0	-0.024	-0.020	23.501	0.019	0.019	0.000	0.000	0.000	0.000
21	A	495	GLU	-1	-0.850	-0.925	24.324	-0.289	-0.289	0.000	0.000	0.000	0.000
22	A	496	ARG	1	0.820	0.893	15.653	0.659	0.659	0.000	0.000	0.000	0.000
23	A	497	THR	0	-0.046	-0.030	22.256	-0.042	-0.042	0.000	0.000	0.000	0.000
24	A	498	THR	0	-0.043	-0.042	24.924	0.006	0.006	0.000	0.000	0.000	0.000
25	A	499	ASP	-1	-0.900	-0.944	28.422	-0.238	-0.238	0.000	0.000	0.000	0.000
26	A	500	GLU	-1	-0.857	-0.913	31.007	-0.240	-0.240	0.000	0.000	0.000	0.000
27	A	501	GLY	0	-0.031	-0.008	27.312	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	502	THR	0	-0.001	0.002	27.118	-0.016	-0.016	0.000	0.000	0.000	0.000
29	A	503	TRP	0	-0.027	-0.026	21.404	-0.028	-0.028	0.000	0.000	0.000	0.000
30	A	504	VAL	0	0.071	0.025	26.825	0.004	0.004	0.000	0.000	0.000	0.000
31	A	505	ALA	0	-0.009	0.016	26.119	0.014	0.014	0.000	0.000	0.000	0.000
32	A	506	GLY	0	0.040	-0.001	23.349	-0.029	-0.029	0.000	0.000	0.000	0.000
33	A	507	VAL	0	-0.028	-0.010	20.481	0.018	0.018	0.000	0.000	0.000	0.000
34	A	508	PHE	0	0.037	0.019	21.113	-0.041	-0.041	0.000	0.000	0.000	0.000
35	A	509	VAL	0	-0.003	-0.009	17.359	0.014	0.014	0.000	0.000	0.000	0.000
36	A	510	TYR	0	0.031	-0.001	20.363	0.000	0.000	0.000	0.000	0.000	0.000
37	A	511	GLY	0	0.036	0.025	21.571	0.000	0.000	0.000	0.000	0.000	0.000
38	A	512	GLY	0	0.001	-0.001	19.965	-0.040	-0.040	0.000	0.000	0.000	0.000
39	A	513	SER	0	-0.005	-0.018	17.693	0.037	0.037	0.000	0.000	0.000	0.000
40	A	514	LYS	1	1.054	1.018	16.914	0.309	0.309	0.000	0.000	0.000	0.000
41	A	515	THR	0	0.029	0.013	13.332	-0.073	-0.073	0.000	0.000	0.000	0.000
42	A	516	SER	0	0.011	0.023	12.976	-0.111	-0.111	0.000	0.000	0.000	0.000
43	A	517	LEU	0	0.006	0.024	13.492	-0.129	-0.129	0.000	0.000	0.000	0.000
44	A	518	TYR	0	-0.005	0.011	8.486	-0.158	-0.158	0.000	0.000	0.000	0.000
45	A	519	ASN	0	-0.058	-0.053	8.664	-0.407	-0.407	0.000	0.000	0.000	0.000
46	A	520	LEU	0	0.072	0.041	9.145	-0.335	-0.335	0.000	0.000	0.000	0.000
47	A	521	ARG	1	0.856	0.944	11.567	0.786	0.786	0.000	0.000	0.000	0.000
48	A	522	ARG	1	0.896	0.944	4.396	1.774	1.874	-0.001	-0.006	-0.092	0.000
49	A	523	GLY	0	0.044	0.018	7.559	-0.370	-0.370	0.000	0.000	0.000	0.000
50	A	524	THR	0	0.009	-0.026	8.449	0.129	0.129	0.000	0.000	0.000	0.000
51	A	525	ALA	0	-0.022	-0.012	9.297	0.097	0.097	0.000	0.000	0.000	0.000
52	A	526	LEU	0	-0.047	-0.015	4.196	0.000	0.071	-0.001	-0.009	-0.061	0.000
53	A	527	ALA	0	-0.007	0.002	8.745	0.215	0.215	0.000	0.000	0.000	0.000
54	A	528	ILE	0	-0.039	-0.015	11.697	0.224	0.224	0.000	0.000	0.000	0.000
55	A	529	PRO	0	0.076	0.049	12.447	0.040	0.040	0.000	0.000	0.000	0.000
56	A	530	GLN	0	0.060	0.044	14.553	0.010	0.010	0.000	0.000	0.000	0.000
57	A	531	CYS	0	-0.039	0.006	15.161	0.046	0.046	0.000	0.000	0.000	0.000
58	A	532	ARG	1	0.885	0.940	16.911	0.595	0.595	0.000	0.000	0.000	0.000
59	A	533	LEU	0	0.009	0.001	13.192	0.010	0.010	0.000	0.000	0.000	0.000
60	A	534	THR	0	0.071	0.046	17.208	0.001	0.001	0.000	0.000	0.000	0.000
61	A	535	PRO	0	0.006	-0.005	17.041	-0.083	-0.083	0.000	0.000	0.000	0.000
62	A	536	LEU	0	-0.046	-0.014	14.691	0.005	0.005	0.000	0.000	0.000	0.000
63	A	537	SER	0	0.006	0.011	18.417	0.038	0.038	0.000	0.000	0.000	0.000
64	A	538	ARG	1	0.830	0.888	22.143	0.211	0.211	0.000	0.000	0.000	0.000
65	A	539	LEU	0	0.037	0.029	24.981	0.005	0.005	0.000	0.000	0.000	0.000
66	A	540	PRO	0	0.048	0.037	27.535	0.009	0.009	0.000	0.000	0.000	0.000
67	A	541	PHE	0	-0.039	-0.026	31.153	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	542	GLY	0	0.024	0.015	33.509	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	543	MET	0	-0.044	-0.033	35.718	0.005	0.005	0.000	0.000	0.000	0.000
70	A	544	ALA	0	-0.011	0.016	38.626	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	545	PRO	0	0.002	-0.003	40.159	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	546	GLY	0	0.034	0.015	43.064	0.003	0.003	0.000	0.000	0.000	0.000
73	A	547	PRO	0	-0.023	-0.026	45.526	0.001	0.001	0.000	0.000	0.000	0.000
74	A	548	GLY	0	0.010	0.026	46.428	0.000	0.000	0.000	0.000	0.000	0.000
75	A	549	PRO	0	-0.023	-0.001	43.766	0.002	0.002	0.000	0.000	0.000	0.000
76	A	550	GLN	0	0.070	0.016	41.020	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	551	PRO	0	-0.031	-0.011	37.300	0.004	0.004	0.000	0.000	0.000	0.000
78	A	552	GLY	0	0.036	0.016	39.617	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	553	PRO	0	0.033	-0.008	36.799	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	554	LEU	0	0.030	0.025	34.519	-0.009	-0.009	0.000	0.000	0.000	0.000
81	A	555	ARG	1	0.910	0.963	33.994	0.116	0.116	0.000	0.000	0.000	0.000
82	A	556	GLU	-1	-0.801	-0.876	28.675	-0.225	-0.225	0.000	0.000	0.000	0.000
83	A	557	SER	0	-0.027	-0.015	28.659	0.011	0.011	0.000	0.000	0.000	0.000
84	A	558	ILE	0	-0.006	-0.029	25.747	-0.013	-0.013	0.000	0.000	0.000	0.000
85	A	559	VAL	0	-0.006	0.009	24.336	-0.024	-0.024	0.000	0.000	0.000	0.000
86	A	560	CYS	0	-0.042	-0.019	20.190	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	561	TYR	0	0.026	-0.005	20.697	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	562	PHE	0	-0.021	-0.022	15.133	-0.030	-0.030	0.000	0.000	0.000	0.000
89	A	563	MET	0	0.020	0.030	19.498	0.017	0.017	0.000	0.000	0.000	0.000
90	A	564	VAL	0	-0.025	-0.015	17.117	-0.057	-0.057	0.000	0.000	0.000	0.000
91	A	565	PHE	0	0.032	0.020	19.473	0.044	0.044	0.000	0.000	0.000	0.000
92	A	566	LEU	0	-0.029	-0.041	19.629	-0.061	-0.061	0.000	0.000	0.000	0.000
93	A	567	GLN	0	0.057	0.039	22.887	0.024	0.024	0.000	0.000	0.000	0.000
94	A	568	THR	0	0.043	0.020	25.280	0.016	0.016	0.000	0.000	0.000	0.000
95	A	569	HIS	0	0.041	0.005	25.817	-0.033	-0.033	0.000	0.000	0.000	0.000
96	A	570	ILE	0	0.019	0.011	27.050	-0.012	-0.012	0.000	0.000	0.000	0.000
97	A	571	PHE	0	0.016	0.009	18.144	-0.028	-0.028	0.000	0.000	0.000	0.000
98	A	572	ALA	0	0.016	0.008	22.307	-0.039	-0.039	0.000	0.000	0.000	0.000
99	A	573	GLU	-1	-0.800	-0.898	23.241	-0.294	-0.294	0.000	0.000	0.000	0.000
100	A	574	VAL	0	0.019	0.009	21.289	-0.011	-0.011	0.000	0.000	0.000	0.000
101	A	575	LEU	0	0.000	-0.002	16.554	-0.033	-0.033	0.000	0.000	0.000	0.000
102	A	576	LYS	1	0.750	0.852	19.686	0.261	0.261	0.000	0.000	0.000	0.000
103	A	577	ASP	-1	-0.780	-0.873	21.983	-0.295	-0.295	0.000	0.000	0.000	0.000
104	A	578	ALA	0	-0.012	-0.003	17.808	0.002	0.002	0.000	0.000	0.000	0.000
105	A	579	ILE	0	-0.002	-0.010	16.332	-0.044	-0.044	0.000	0.000	0.000	0.000
106	A	580	LYS	1	0.859	0.917	18.228	0.285	0.285	0.000	0.000	0.000	0.000
107	A	581	ASP	-1	-0.789	-0.880	20.731	-0.296	-0.296	0.000	0.000	0.000	0.000
108	A	582	LEU	0	-0.011	0.011	12.830	0.020	0.020	0.000	0.000	0.000	0.000
109	A	583	VAL	0	-0.053	-0.034	16.407	-0.012	-0.012	0.000	0.000	0.000	0.000
110	A	584	MET	0	0.003	0.006	18.327	0.044	0.044	0.000	0.000	0.000	0.000
111	A	585	THR	0	-0.030	-0.008	18.960	0.022	0.022	0.000	0.000	0.000	0.000
112	A	586	LYS	1	0.800	0.894	14.572	0.429	0.429	0.000	0.000	0.000	0.000
113	A	587	PRO	0	0.062	0.028	17.368	0.019	0.019	0.000	0.000	0.000	0.000
114	A	588	ALA	0	0.059	0.043	19.567	-0.050	-0.050	0.000	0.000	0.000	0.000
115	A	589	PRO	0	-0.028	-0.033	18.096	0.012	0.012	0.000	0.000	0.000	0.000
116	A	590	THR	0	-0.016	-0.020	15.440	-0.005	-0.005	0.000	0.000	0.000	0.000
117	A	591	CYS	0	0.008	0.018	18.132	-0.016	-0.016	0.000	0.000	0.000	0.000
118	A	592	ASN	0	-0.001	0.008	21.302	0.019	0.019	0.000	0.000	0.000	0.000
119	A	593	ILE	0	-0.053	-0.032	16.398	0.000	0.000	0.000	0.000	0.000	0.000
120	A	594	ARG	1	0.890	0.959	20.748	0.283	0.283	0.000	0.000	0.000	0.000
121	A	595	VAL	0	0.002	-0.005	20.606	-0.031	-0.031	0.000	0.000	0.000	0.000
122	A	596	THR	0	-0.040	-0.017	22.961	0.037	0.037	0.000	0.000	0.000	0.000
123	A	597	VAL	0	0.044	0.036	24.492	-0.033	-0.033	0.000	0.000	0.000	0.000
124	A	598	CYS	0	-0.066	-0.023	26.193	0.011	0.011	0.000	0.000	0.000	0.000
125	A	599	SER	0	0.036	0.014	27.694	-0.017	-0.017	0.000	0.000	0.000	0.000
126	A	600	PHE	0	-0.050	-0.038	25.637	-0.005	-0.005	0.000	0.000	0.000	0.000
127	A	601	ASP	-1	-0.910	-0.938	31.357	-0.202	-0.202	0.000	0.000	0.000	0.000
128	A	602	ASP	-1	-0.901	-0.945	34.938	-0.181	-0.181	0.000	0.000	0.000	0.000
129	A	603	GLY	0	-0.051	-0.022	30.778	-0.004	-0.004	0.000	0.000	0.000	0.000
130	A	604	VAL	0	-0.062	-0.041	26.545	0.002	0.002	0.000	0.000	0.000	0.000
131	A	605	ASP	-1	-0.897	-0.947	28.110	-0.274	-0.274	0.000	0.000	0.000	0.000
132	A	606	LEU	0	-0.084	-0.047	22.327	-0.010	-0.010	0.000	0.000	0.000	0.000
133	A	607	PRO	0	-0.004	0.007	24.821	0.005	0.005	0.000	0.000	0.000	0.000
134	A	608	PRO	0	0.018	0.013	24.954	-0.029	-0.029	0.000	0.000	0.000	0.000
135	A	609	TRP	0	-0.032	-0.021	19.831	-0.007	-0.007	0.000	0.000	0.000	0.000
136	A	610	PHE	0	0.010	-0.006	24.387	0.006	0.006	0.000	0.000	0.000	0.000
137	A	611	PRO	0	-0.012	0.009	22.250	0.020	0.020	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:475:ASN)